Related papers: On Metropolis Integrators for Molecular Dynamics
The simulation of multi-body systems with frictional contacts is a fundamental tool for many fields, such as robotics, computer graphics, and mechanics. Hard frictional contacts are particularly troublesome to simulate because they make the…
Molecular dynamics simulation is a proven technique for computing and visualizing the time-resolved motion of macromolecules at atomic resolution. The MDsrv is a tool that streams MD trajectories and displays them interactively in web…
We propose a method for multi-scale hybrid simulations of molecular dynamics (MD) and computational fluid dynamics (CFD). In the method, usual lattice-mesh based simulations are applied for CFD level, but each lattice is associated with a…
Classical Molecular Dynamics (MD) simulations are employed as a tool to investigate structural properties of ice crystals under several temperature and pressure conditions. All ice crystal phases are analyzed by means of a computational…
We propose a fast and general predecision scheme for Metropolis Monte Carlo simulation of $d$-dimensional long-range interacting lattice models. For potentials of the form $V(r)=r^{-d-\sigma}$, this reduces the computational complexity from…
The multiple Try Metropolis (MTM) algorithm is an advanced MCMC technique based on drawing and testing several candidates at each iteration of the algorithm. One of them is selected according to certain weights and then it is tested…
We consider deployment of the particle filter on modern massively parallel hardware architectures, such as Graphics Processing Units (GPUs), with a focus on the resampling stage. While standard multinomial and stratified resamplers require…
Molecular dynamics (MD) simulations of the zeta potential are so poor that it has become common to term their predictions 'apparent'. Here we demonstrate how zeta potentials that agree with measured values can be calculated by: (1)…
Emergent phenomena share the fascinating property of not being obvious consequences of the design of the system in which they appear. This characteristic is no less relevant when attempting to simulate such phenomena, given that the outcome…
Neural network potentials (NNPs) enable large-scale molecular dynamics (MD) simulations of systems containing >10,000 atoms with the accuracy comparable to ab initio methods and play a crucial role in material studies. Although NNPs are…
The simulation of systems that act on multiple time scales is challenging. A stable integration of the fast dynamics requires a highly accurate approximation whereas for the simulation of the slow part, a coarser approximation is accurate…
The growing interest in the dynamical properties of colloidal suspensions, both in equilibrium and under an external drive such as shear or pressure flow, requires the development of accurate methods to correctly include hydrodynamic…
We introduce JAX MD, a software package for performing differentiable physics simulations with a focus on molecular dynamics. JAX MD includes a number of physics simulation environments, as well as interaction potentials and neural networks…
Molecular spintronics devices (MSDs) are highly promising candidates for enabling quantum computation and revolutionizing computer logic and memory. An advanced MSD will require the placement of magnetic molecules between the two…
This paper proposes several explicit and implicit multistep frequency response optimized integrators considering first or second order derivative. A prediction-based method aiming at accelerating a novel power system transient simulation…
Molecular dynamics (MD) simulation is one of the past decade's most important tools for enabling biology scientists and researchers to explore human health and diseases. However, due to the computation complexity of the MD algorithm, it…
The paradigm that the primary amino acid sequence prescribes structure and thus function has for a long time been central to the understanding of protein science. Though the theory is supported by the behaviour of most structured proteins,…
Molecular dynamics (MD) simulations enable the description of ma- terial properties and processes with atomistic detail by numerically solv- ing the time evolution of every atom in the system. We introduce Poly- merModeler, a…
A general framework for performing event-driven simulations of systems with semi-flexible or rigid bodies interacting under impulsive torques and forces is outlined. Two different approaches are presented. In the first, the dynamics and…
A novel Stochastic Event-Driven Molecular Dynamics (SEDMD) algorithm is developed for the simulation of polymer chains suspended in a solvent. The polymers are represented as chains of hard spheres tethered by square wells and interact with…